Frequently Asked Questions

FAQ

2′‑OMe vs 2′‑F for siRNA?

Mix both: 2′‑F increases A‑form bias and Tm; 2′‑OMe is helpful for safety and reduces off‑targeting, especially in the seed region.

2′-OMe vs 2′-F—when should I choose each?

2′-OMe favors immune dampening and stability; 2′-F improves potency and stability. Mixed patterns in the wings are common; we’ll tailor to your readouts.

21mer vs. 27mer siRNA Design?

21mer siRNAs: Mimic Dicer products, bypass Dicer, and enter RISC directly.

27mer Dicer-substrate siRNAs: Require Dicer processing, improving RISC loading and gene knockdown efficiency.

5′ vs 3′ vs internal tagging — what should I choose?

Default to 5′/3′ for accessibility; use internal dT‑linkers when mid‑strand placement is required. Add C6–C12/PEG spacers to reduce steric hindrance.

5′/3′ vs. internal lipid placement — how do I choose?

Termini (5′/3′) minimize impact on hybridization and are easiest to QC. Internal placement is possible with appropriate spacers (e.g., PEG) but should be piloted to confirm Tm and activity.

ADC: cleavable vs non‑cleavable — how to choose?

Use cleavable (disulfide, hydrazone, dipeptide/self‑immolative) when intracellular release is needed; choose non‑cleavable when maximal durability is required.

Any guidance for in vivo use?

Choose lipids that match the target tissue and delivery route (e.g., GalNAc for liver). Validate PK/PD, assess immunogenicity, and consider LNP or micelle formulation for certain lipids (DSPE-PEG, DAG, phospholipids).

Any quick probe design rules of thumb?

  • Primer Tm typically 58–62 °C; probe Tm about 7–10 °C higher than primers.
  • Avoid G at the reporter-labeled 5′ end; avoid long runs of G/C (≥4).
  • Keep amplicons short (e.g., 70–150 bp) for fast, efficient RT-qPCR.
  • Typical starting concentrations: primers 200–500 nM; probe 100–250 nM (optimize empirically).

Any special considerations for ddPCR?

Use dark quenchers with tight spectral separation and verify droplet reader channels. Pilot dye/quencher combinations under final conditions.

Any special storage?

Store dry and protected from light; avoid prolonged UV exposure prior to use. Standard –20 °C recommended.

Are acetylated peptides synthetic?

Yes. Research-grade acetylated peptides are typically chemically synthesized so acetylation is installed at defined residue positions and stoichiometry. Synthetic acetylated peptides avoid heterogeneity and are preferred for mechanistic studies, quantitative LC–MS workflows, and assay controls.

Are ASOs toxic to cells?

Toxicity depends on sequence, chemistry, delivery method, and concentration. PS-ASOs may bind non-specifically to proteins and activate immune receptors.

Are beacons suitable for multiplexing?

Yes. Choose **non-overlapping dyes**, balance brightness across channels, and validate NTC/no-probe controls for flat baselines.

Are branched peptides limited to lysine MAP peptides?

No. Lysine-based MAP peptides are common, but branched peptides can also be designed using alternative diamino acid branch points (Dap/Dab/Orn), dendrimeric or small-molecule cores, and post-synthetic branching chemistries (e.g., cysteine/thioether or click chemistry). The best strategy depends on the required spacing/geometry, steric congestion risk, solubility, stability, and your downstream application.

Are cell-penetrating peptides (CPPs) considered delivery modifiers?

Yes. CPPs are peptides (not small molecules), but they are widely grouped under delivery modifiers because they enhance cellular uptake and intracellular trafficking. CPP–oligo conjugates are common for splice-switching oligos (SSO), PMO, and peptide–PMO programs.

Are cleavable linkers available for oncology peptide–drug conjugates?

Cleavable linker concepts (e.g., enzyme-, pH-, or redox-responsive) can be evaluated when controlled payload release is desired. Linker selection is guided by the oncology drug, peptide sequence, and intended biological environment.

Are DX peptides intended for clinical use?

Intended use depends on your final application and regulatory pathway. This page describes quality system and documentation support; please discuss your intended use and requirements with our team so we can align the appropriate grade and deliverables.

Are fluorophore-labeled peptides the same as imaging peptides?

Fluorophore-labeled peptides are one major type of imaging peptide. “Imaging conjugates” is broader and can include NIR dyes, chelator-enabled (radiolabel-compatible) precursors, or dual-label combinations (project-dependent).

Are helical peptides always stapled peptides?

No. Stapled peptides are one subset that use hydrocarbon crosslinks. Helical peptides may also be stabilized with lactam bridges, disulfide/thioether constraints, helix-promoting residues (e.g., Aib), or backbone modifications.

Are lipid conjugates the same as drug conjugates?

Typically no. Lipid conjugates primarily enhance delivery or PK. “Drug conjugates” generally refer to pharmacologically active small-molecule payloads linked to the oligo.

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